How to mask stabilized footage
The first thing I suggest is turn off autoscale and do the scaling with a Transform node in the compositor, that way you'll have more control on the final output and composition.
You do have access to the Tracker information by adding a Track Position node and manually typing the name of the tracker you want to use. (Keep in mind that that same tracker has to be part of the set of trackers used for the 2D stabilization)
Some manual positioning might be necessary to place the mask on the right place, but after that the mask should follow the stabilized footage.

Here's a possible Node arrangement: